chr6-108698829-G-T

Variant names:

• chr6-108698829-G-T
• rs479744

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.323 in 151,960 control chromosomes in the GnomAD database, including 9,985 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (9985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48970 AN: 151842 Hom.: 9962 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.308

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.323 AC: 49040 AN: 151960 Hom.: 9985 Cov.: 32 AF XY: 0.322 AC XY: 23944 AN XY: 74266

African (AFR) AF: 0.575 AC: 23787 AN: 41400

American (AMR) AF: 0.281 AC: 4293 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 585 AN: 3472

East Asian (EAS) AF: 0.147 AC: 760 AN: 5156

South Asian (SAS) AF: 0.401 AC: 1925 AN: 4806

European-Finnish (FIN) AF: 0.241 AC: 2543 AN: 10566

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14236 AN: 67962

Other (OTH) AF: 0.305 AC: 642 AN: 2106

Alfa AF: 0.243 Hom.: 9662

Bravo AF: 0.335

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs479744; hg19: chr6-109020032; COSMIC: COSV60265013;